Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024625.1 Corchorus olitorius cultivar O-4 contig24658, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 22057
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:4511 original size:11 final size:10

Alignment explanation


    Indices: 4495--4541  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       4485 AAGTTTATGT

                       
       4495 TTGAAGACTCA
          1 TTGAAGA-TCA

                    * 
       4506 TTGAAGATAA
          1 TTGAAGATCA

                       
       4516 TTTGAAGAT--
          1 -TTGAAGATCA

                      
       4525 TTGAAGATCA
          1 TTGAAGATCA

                   
       4535 TTGAAGA
          1 TTGAAGA

       4542 ATTATATCAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    8  0.25
  10    9  0.28
  11   15  0.47

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32


Consensus pattern (10 bp):   
TTGAAGATCA

Found at i:4530 original size:19 final size:18

Alignment explanation


    Indices: 4506--4541  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4496 TGAAGACTCA

                               
       4506 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       4525 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       4542 ATTATATCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:9134 original size:21 final size:21

Alignment explanation


    Indices: 9108--9148  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       9098 AGAAAAACCC

                                  
       9108 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
       9129 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

       9149 AGGGCTTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:19537 original size:34 final size:34

Alignment explanation


    Indices: 19494--19580  Score: 156
    Period size: 34  Copynumber: 2.6  Consensus size: 34

      19484 TTTTTTTAAA

                          **                  
      19494 TTTAGGGAAAGATCTTATCCAGTCTTCAAGGTTT
          1 TTTAGGGAAAGATCCCATCCAGTCTTCAAGGTTT

                                              
      19528 TTTAGGGAAAGATCCCATCCAGTCTTCAAGGTTT
          1 TTTAGGGAAAGATCCCATCCAGTCTTCAAGGTTT

                               
      19562 TTTAGGGAAAGATCCCATC
          1 TTTAGGGAAAGATCCCATC

      19581 AAGTTTTTCA


Statistics
Matches: 51,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  34   51  1.00

ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33


Consensus pattern (34 bp):   
TTTAGGGAAAGATCCCATCCAGTCTTCAAGGTTT

Found at i:19609 original size:39 final size:34

Alignment explanation


    Indices: 19494--19620  Score: 146
    Period size: 34  Copynumber: 3.6  Consensus size: 34

      19484 TTTTTTTAAA

                          **   *              
      19494 TTTAGGGAAAGATCTTATCCAGTCTTCAAGGTTT
          1 TTTAGGGAAAGATCCCATCAAGTCTTCAAGGTTT

                               *              
      19528 TTTAGGGAAAGATCCCATCCAGTCTTCAAGGTTT
          1 TTTAGGGAAAGATCCCATCAAGTCTTCAAGGTTT

                                    *        *   
      19562 TTTAGGGAAAGATCCCATCAAGTTTTTCAGAAGTTTT
          1 TTTAGGGAAAGATCCCATCAAG-TCTTC--AAGGTTT

                           *      
      19599 AATTTAGGGAAAGATTCCATCA
          1 --TTTAGGGAAAGATCCCATCA

      19621 TCCAGTAGTT


Statistics
Matches: 82,  Mismatches: 6, Indels: 5
        0.88            0.06        0.05

Matches are distributed among these distances:
  34   53  0.65
  35    4  0.05
  37    6  0.07
  39   19  0.23

ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35


Consensus pattern (34 bp):   
TTTAGGGAAAGATCCCATCAAGTCTTCAAGGTTT
Done.